Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.14

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-02-17, 11:30 CET based on data in:

        General Statistics

        Showing 331/331 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        A006850198_172407_S137_L001_R1_001
        38.4%
        33%
        6.6
        A006850198_172407_S137_L002_R1_001
        38.4%
        33%
        6.6
        A006850198_172410_S138_L001_R1_001
        41.3%
        34%
        6.2
        A006850198_172410_S138_L002_R1_001
        41.2%
        34%
        6.2
        A006850198_172412_S139_L001_R1_001
        59.2%
        38%
        6.3
        A006850198_172412_S139_L002_R1_001
        58.8%
        38%
        6.3
        A006850198_172414_S140_L001_R1_001
        62.1%
        38%
        7.9
        A006850198_172414_S140_L002_R1_001
        61.6%
        38%
        7.9
        A006850198_172416_S141_L001_R1_001
        50.9%
        36%
        6.7
        A006850198_172416_S141_L002_R1_001
        50.9%
        36%
        6.7
        A006850198_172418_S142_L001_R1_001
        65.7%
        40%
        6.7
        A006850198_172418_S142_L002_R1_001
        65.7%
        40%
        6.7
        A006850198_172420_S143_L001_R1_001
        41.5%
        33%
        7.3
        A006850198_172420_S143_L002_R1_001
        41.3%
        33%
        7.3
        A006850198_172422_S144_L001_R1_001
        50.8%
        35%
        6.3
        A006850198_172422_S144_L002_R1_001
        50.8%
        35%
        6.3
        A006850198_172424_S145_L001_R1_001
        38.7%
        34%
        6.2
        A006850198_172424_S145_L002_R1_001
        38.6%
        34%
        6.2
        A006850198_172426_S146_L001_R1_001
        41.0%
        33%
        9.1
        A006850198_172426_S146_L002_R1_001
        41.0%
        33%
        9.1
        A006850198_172428_S147_L001_R1_001
        43.8%
        35%
        7.1
        A006850198_172428_S147_L002_R1_001
        43.6%
        35%
        7.1
        A006850198_172430_S148_L001_R1_001
        41.9%
        34%
        7.4
        A006850198_172430_S148_L002_R1_001
        41.9%
        34%
        7.4
        A006850198_172432_S149_L001_R1_001
        50.1%
        37%
        8.0
        A006850198_172432_S149_L002_R1_001
        49.8%
        37%
        8.0
        A006850198_172434_S150_L001_R1_001
        50.8%
        38%
        6.2
        A006850198_172434_S150_L002_R1_001
        50.7%
        38%
        6.2
        A006850198_172436_S151_L001_R1_001
        42.8%
        34%
        7.0
        A006850198_172436_S151_L002_R1_001
        42.5%
        34%
        7.0
        A006850198_172438_S152_L001_R1_001
        41.9%
        34%
        6.2
        A006850198_172438_S152_L002_R1_001
        41.9%
        34%
        6.2
        A006850198_172440_S153_L001_R1_001
        44.5%
        35%
        6.7
        A006850198_172440_S153_L002_R1_001
        44.4%
        35%
        6.7
        A006850198_172442_S154_L001_R1_001
        47.8%
        37%
        5.5
        A006850198_172442_S154_L002_R1_001
        47.6%
        37%
        5.5
        A006850198_172444_S155_L001_R1_001
        44.1%
        35%
        6.8
        A006850198_172444_S155_L002_R1_001
        44.0%
        35%
        6.8
        A006850198_172446_S156_L001_R1_001
        43.1%
        35%
        5.5
        A006850198_172446_S156_L002_R1_001
        42.7%
        35%
        5.5
        A006850198_172448_S157_L001_R1_001
        50.4%
        35%
        7.2
        A006850198_172448_S157_L002_R1_001
        50.4%
        36%
        7.2
        A006850198_172450_S158_L001_R1_001
        38.4%
        34%
        6.4
        A006850198_172450_S158_L002_R1_001
        38.3%
        34%
        6.4
        A006850198_172452_S159_L001_R1_001
        47.8%
        35%
        6.1
        A006850198_172452_S159_L002_R1_001
        47.7%
        36%
        6.1
        A006850198_172454_S160_L001_R1_001
        46.0%
        34%
        6.6
        A006850198_172454_S160_L002_R1_001
        46.0%
        34%
        6.6
        A006850198_172456_S161_L001_R1_001
        46.4%
        36%
        6.7
        A006850198_172456_S161_L002_R1_001
        46.3%
        36%
        6.7
        A006850198_172458_S162_L001_R1_001
        47.4%
        36%
        6.1
        A006850198_172458_S162_L002_R1_001
        47.0%
        36%
        6.1
        A006850198_172460_S163_L001_R1_001
        44.9%
        35%
        6.4
        A006850198_172460_S163_L002_R1_001
        44.7%
        35%
        6.4
        A006850198_172462_S164_L001_R1_001
        47.0%
        36%
        7.0
        A006850198_172462_S164_L002_R1_001
        47.1%
        36%
        7.0
        A006850198_172464_S165_L001_R1_001
        44.4%
        35%
        7.8
        A006850198_172464_S165_L002_R1_001
        44.3%
        35%
        7.8
        A006850198_172466_S166_L001_R1_001
        42.3%
        34%
        5.6
        A006850198_172466_S166_L002_R1_001
        42.0%
        34%
        5.6
        A006850198_172468_S167_L001_R1_001
        39.4%
        34%
        6.8
        A006850198_172468_S167_L002_R1_001
        39.4%
        34%
        6.8
        A006850198_172470_S168_L001_R1_001
        38.7%
        33%
        8.3
        A006850198_172470_S168_L002_R1_001
        38.6%
        33%
        8.3
        A006850198_172472_S169_L001_R1_001
        43.7%
        35%
        7.5
        A006850198_172472_S169_L002_R1_001
        43.8%
        35%
        7.5
        A006850198_172474_S170_L001_R1_001
        46.1%
        31%
        7.1
        A006850198_172474_S170_L002_R1_001
        45.9%
        31%
        7.1
        A006850198_172476_S171_L001_R1_001
        40.1%
        36%
        4.4
        A006850198_172476_S171_L002_R1_001
        39.9%
        36%
        4.4
        A006850198_172478_S172_L001_R1_001
        44.9%
        35%
        6.6
        A006850198_172478_S172_L002_R1_001
        45.0%
        35%
        6.6
        A006850198_172480_S173_L001_R1_001
        42.6%
        35%
        6.3
        A006850198_172480_S173_L002_R1_001
        42.4%
        35%
        6.3
        A006850198_172482_S174_L001_R1_001
        38.9%
        34%
        6.0
        A006850198_172482_S174_L002_R1_001
        38.7%
        34%
        6.0
        A006850198_172484_S175_L001_R1_001
        37.5%
        33%
        7.0
        A006850198_172484_S175_L002_R1_001
        37.2%
        33%
        7.0
        A006850198_172486_S176_L001_R1_001
        37.1%
        32%
        8.8
        A006850198_172486_S176_L002_R1_001
        36.8%
        32%
        8.8
        A006850198_172488_S177_L001_R1_001
        39.2%
        33%
        7.3
        A006850198_172488_S177_L002_R1_001
        39.1%
        33%
        7.3
        A006850198_172490_S178_L001_R1_001
        40.8%
        35%
        5.7
        A006850198_172490_S178_L002_R1_001
        40.6%
        35%
        5.7
        A006850198_172492_S179_L001_R1_001
        43.4%
        35%
        6.9
        A006850198_172492_S179_L002_R1_001
        43.5%
        35%
        6.9
        A006850198_172494_S180_L001_R1_001
        43.5%
        35%
        6.6
        A006850198_172494_S180_L002_R1_001
        43.4%
        35%
        6.6
        A006850198_172496_S181_L001_R1_001
        39.5%
        33%
        6.4
        A006850198_172496_S181_L002_R1_001
        39.4%
        33%
        6.4
        A006850198_172498_S182_L001_R1_001
        42.5%
        35%
        5.4
        A006850198_172498_S182_L002_R1_001
        42.3%
        35%
        5.4
        A006850198_172500_S183_L001_R1_001
        36.6%
        33%
        6.7
        A006850198_172500_S183_L002_R1_001
        36.6%
        33%
        6.7
        A006850198_172502_S184_L001_R1_001
        37.3%
        32%
        6.8
        A006850198_172502_S184_L002_R1_001
        37.1%
        32%
        6.8
        A006850198_172504_S185_L001_R1_001
        43.7%
        36%
        4.6
        A006850198_172504_S185_L002_R1_001
        43.6%
        37%
        4.6
        A006850198_172507_S186_L001_R1_001
        47.5%
        36%
        6.3
        A006850198_172507_S186_L002_R1_001
        47.4%
        36%
        6.3
        A006850198_172509_S187_L001_R1_001
        39.9%
        36%
        3.5
        A006850198_172509_S187_L002_R1_001
        39.6%
        36%
        3.5
        A006850198_172511_S188_L001_R1_001
        44.6%
        37%
        4.4
        A006850198_172511_S188_L002_R1_001
        44.3%
        37%
        4.4
        A006850198_172513_S189_L001_R1_001
        33.1%
        34%
        3.1
        A006850198_172513_S189_L002_R1_001
        32.6%
        34%
        3.1
        A006850198_172515_S190_L001_R1_001
        70.4%
        41%
        3.4
        A006850198_172515_S190_L002_R1_001
        70.3%
        41%
        3.4
        A006850198_172517_S191_L001_R1_001
        66.5%
        41%
        3.7
        A006850198_172517_S191_L002_R1_001
        66.2%
        41%
        3.7
        A006850198_172519_S192_L001_R1_001
        56.0%
        39%
        3.3
        A006850198_172519_S192_L002_R1_001
        56.0%
        39%
        3.3
        A006850198_172521_S193_L001_R1_001
        56.2%
        37%
        8.2
        A006850198_172521_S193_L002_R1_001
        56.0%
        38%
        8.2
        A006850198_172523_S194_L001_R1_001
        50.7%
        37%
        8.0
        A006850198_172523_S194_L002_R1_001
        50.6%
        37%
        8.0
        A006850198_172525_S195_L001_R1_001
        68.1%
        40%
        8.7
        A006850198_172525_S195_L002_R1_001
        68.1%
        40%
        8.7
        A006850198_172527_S196_L001_R1_001
        71.3%
        40%
        7.5
        A006850198_172527_S196_L002_R1_001
        71.0%
        40%
        7.5
        A006850198_172529_S197_L001_R1_001
        51.1%
        37%
        8.0
        A006850198_172529_S197_L002_R1_001
        51.0%
        37%
        8.0
        A006850198_172531_S198_L001_R1_001
        67.8%
        41%
        9.3
        A006850198_172531_S198_L002_R1_001
        67.6%
        41%
        9.3
        A006850198_172533_S199_L001_R1_001
        64.9%
        39%
        8.6
        A006850198_172533_S199_L002_R1_001
        64.8%
        39%
        8.6
        A006850198_172535_S200_L001_R1_001
        66.7%
        40%
        9.6
        A006850198_172535_S200_L002_R1_001
        66.4%
        40%
        9.6
        A006850198_172537_S201_L001_R1_001
        74.2%
        43%
        8.2
        A006850198_172537_S201_L002_R1_001
        74.1%
        43%
        8.2
        A006850198_172539_S202_L001_R1_001
        63.3%
        40%
        3.6
        A006850198_172539_S202_L002_R1_001
        63.3%
        40%
        3.6
        A006850198_172541_S203_L001_R1_001
        62.8%
        40%
        3.4
        A006850198_172541_S203_L002_R1_001
        62.4%
        40%
        3.4
        A006850198_172543_S204_L001_R1_001
        61.6%
        39%
        4.0
        A006850198_172543_S204_L002_R1_001
        61.4%
        39%
        4.0
        A006850198_172545_S205_L001_R1_001
        64.4%
        40%
        4.1
        A006850198_172545_S205_L002_R1_001
        64.1%
        40%
        4.1
        A006850198_172547_S206_L001_R1_001
        49.2%
        37%
        7.8
        A006850198_172547_S206_L002_R1_001
        49.2%
        37%
        7.8
        A006850198_172549_S207_L001_R1_001
        72.8%
        40%
        10.2
        A006850198_172549_S207_L002_R1_001
        72.6%
        40%
        10.2
        A006850198_172551_S208_L001_R1_001
        69.3%
        40%
        8.0
        A006850198_172551_S208_L002_R1_001
        69.2%
        40%
        8.0
        A006850198_172553_S209_L001_R1_001
        71.1%
        40%
        7.0
        A006850198_172553_S209_L002_R1_001
        71.0%
        40%
        7.0
        A006850198_172555_S210_L001_R1_001
        52.0%
        35%
        7.5
        A006850198_172555_S210_L002_R1_001
        51.9%
        35%
        7.5
        A006850198_172557_S211_L001_R1_001
        70.6%
        41%
        9.9
        A006850198_172557_S211_L002_R1_001
        70.5%
        41%
        9.9
        A006850198_172559_S212_L001_R1_001
        72.9%
        42%
        9.0
        A006850198_172559_S212_L002_R1_001
        72.7%
        42%
        9.0
        A006850198_172561_S213_L001_R1_001
        65.3%
        41%
        3.5
        A006850198_172561_S213_L002_R1_001
        65.1%
        41%
        3.5
        A006850198_172563_S214_L001_R1_001
        62.6%
        40%
        4.6
        A006850198_172563_S214_L002_R1_001
        62.5%
        40%
        4.6
        A006850198_172565_S215_L001_R1_001
        53.0%
        37%
        3.9
        A006850198_172565_S215_L002_R1_001
        53.0%
        37%
        3.9
        A006850198_172567_S216_L001_R1_001
        66.0%
        40%
        6.4
        A006850198_172567_S216_L002_R1_001
        65.8%
        40%
        6.4
        A006850198_172569_S217_L001_R1_001
        71.0%
        41%
        9.9
        A006850198_172569_S217_L002_R1_001
        70.9%
        41%
        9.9
        A006850198_172571_S218_L001_R1_001
        63.1%
        40%
        4.1
        A006850198_172571_S218_L002_R1_001
        62.9%
        40%
        4.1
        A006850198_172573_S219_L001_R1_001
        60.8%
        40%
        3.9
        A006850198_172573_S219_L002_R1_001
        60.7%
        40%
        3.9
        A006850198_172575_S220_L001_R1_001
        47.4%
        32%
        2.8
        A006850198_172575_S220_L002_R1_001
        46.9%
        32%
        2.8
        A006850198_172577_S221_L001_R1_001
        64.8%
        39%
        9.0
        A006850198_172577_S221_L002_R1_001
        64.6%
        40%
        9.0
        A006850198_172579_S222_L001_R1_001
        69.2%
        39%
        8.4
        A006850198_172579_S222_L002_R1_001
        69.0%
        39%
        8.4
        A006850198_172581_S223_L001_R1_001
        74.2%
        35%
        7.5
        A006850198_172581_S223_L002_R1_001
        74.0%
        35%
        7.5
        A006850198_172583_S224_L001_R1_001
        67.6%
        39%
        10.6
        A006850198_172583_S224_L002_R1_001
        67.4%
        39%
        10.6
        A006850198_172585_S225_L001_R1_001
        66.8%
        39%
        8.1
        A006850198_172585_S225_L002_R1_001
        66.6%
        39%
        8.1
        A006850198_172587_S226_L001_R1_001
        70.6%
        40%
        9.5
        A006850198_172587_S226_L002_R1_001
        70.4%
        40%
        9.5
        A006850198_172589_S227_L001_R1_001
        73.3%
        40%
        9.2
        A006850198_172589_S227_L002_R1_001
        73.0%
        40%
        9.2
        A006850198_172591_S228_L001_R1_001
        73.6%
        40%
        9.2
        A006850198_172591_S228_L002_R1_001
        73.3%
        40%
        9.2
        A006850198_172593_S229_L001_R1_001
        83.5%
        30%
        6.0
        A006850198_172593_S229_L002_R1_001
        83.1%
        30%
        6.0
        A006850198_172595_S230_L001_R1_001
        70.5%
        39%
        10.2
        A006850198_172595_S230_L002_R1_001
        70.0%
        39%
        10.2
        A006850198_172597_S231_L001_R1_001
        70.4%
        39%
        9.3
        A006850198_172597_S231_L002_R1_001
        70.2%
        39%
        9.3
        A006850198_172599_S232_L001_R1_001
        71.8%
        39%
        8.4
        A006850198_172599_S232_L002_R1_001
        71.6%
        39%
        8.4
        A006850198_172601_S233_L001_R1_001
        67.7%
        40%
        7.3
        A006850198_172601_S233_L002_R1_001
        67.7%
        40%
        7.3
        A006850198_172604_S234_L001_R1_001
        74.0%
        40%
        7.7
        A006850198_172604_S234_L002_R1_001
        73.7%
        40%
        7.7
        A006850198_172606_S235_L001_R1_001
        68.7%
        39%
        6.8
        A006850198_172606_S235_L002_R1_001
        68.6%
        39%
        6.8
        A006850198_172608_S236_L001_R1_001
        67.2%
        38%
        8.0
        A006850198_172608_S236_L002_R1_001
        66.9%
        38%
        8.0
        A006850198_172610_S237_L001_R1_001
        64.4%
        39%
        6.1
        A006850198_172610_S237_L002_R1_001
        64.1%
        39%
        6.1
        A006850198_172612_S238_L001_R1_001
        53.8%
        35%
        8.0
        A006850198_172612_S238_L002_R1_001
        53.6%
        35%
        8.0
        A006850198_172614_S239_L001_R1_001
        50.6%
        35%
        7.0
        A006850198_172614_S239_L002_R1_001
        50.4%
        35%
        7.0
        A006850198_172616_S240_L001_R1_001
        71.3%
        40%
        5.7
        A006850198_172616_S240_L002_R1_001
        71.0%
        40%
        5.7
        A006850198_172618_S241_L001_R1_001
        76.7%
        41%
        7.0
        A006850198_172618_S241_L002_R1_001
        76.5%
        41%
        7.0
        A006850198_172620_S242_L001_R1_001
        78.5%
        41%
        6.8
        A006850198_172620_S242_L002_R1_001
        78.3%
        41%
        6.8
        A006850198_172622_S243_L001_R1_001
        79.9%
        40%
        7.8
        A006850198_172622_S243_L002_R1_001
        79.8%
        40%
        7.8
        A006850198_172624_S244_L001_R1_001
        83.0%
        41%
        6.1
        A006850198_172624_S244_L002_R1_001
        82.7%
        41%
        6.1
        A006850198_172626_S245_L001_R1_001
        79.0%
        41%
        7.0
        A006850198_172626_S245_L002_R1_001
        79.0%
        41%
        7.0
        A006850198_172628_S246_L001_R1_001
        83.4%
        42%
        6.1
        A006850198_172628_S246_L002_R1_001
        83.3%
        42%
        6.1
        A006850198_172630_S247_L001_R1_001
        83.9%
        38%
        6.6
        A006850198_172630_S247_L002_R1_001
        83.7%
        38%
        6.6
        A006850198_172632_S248_L001_R1_001
        78.4%
        38%
        5.4
        A006850198_172632_S248_L002_R1_001
        78.4%
        38%
        5.4
        A006850198_172634_S249_L001_R1_001
        78.0%
        39%
        6.7
        A006850198_172634_S249_L002_R1_001
        77.9%
        39%
        6.7
        A006850198_172636_S250_L001_R1_001
        81.8%
        42%
        6.4
        A006850198_172636_S250_L002_R1_001
        81.5%
        42%
        6.4
        A006850198_172638_S251_L001_R1_001
        80.2%
        40%
        7.0
        A006850198_172638_S251_L002_R1_001
        80.1%
        40%
        7.0
        A006850198_172640_S252_L001_R1_001
        86.2%
        41%
        6.6
        A006850198_172640_S252_L002_R1_001
        86.1%
        41%
        6.6
        A006850198_172642_S253_L001_R1_001
        77.5%
        40%
        4.5
        A006850198_172642_S253_L002_R1_001
        77.3%
        40%
        4.5
        A006850198_172644_S254_L001_R1_001
        76.0%
        40%
        6.1
        A006850198_172644_S254_L002_R1_001
        75.8%
        40%
        6.1
        A006850198_172646_S255_L001_R1_001
        81.1%
        41%
        7.4
        A006850198_172646_S255_L002_R1_001
        81.0%
        41%
        7.4
        A006850198_172648_S256_L001_R1_001
        76.6%
        40%
        4.4
        A006850198_172648_S256_L002_R1_001
        76.6%
        40%
        4.4
        A006850198_172650_S257_L001_R1_001
        85.4%
        39%
        5.9
        A006850198_172650_S257_L002_R1_001
        85.3%
        39%
        5.9
        A006850198_172652_S258_L001_R1_001
        88.7%
        34%
        7.4
        A006850198_172652_S258_L002_R1_001
        88.5%
        34%
        7.4
        A006850198_172654_S259_L001_R1_001
        78.5%
        41%
        6.1
        A006850198_172654_S259_L002_R1_001
        78.3%
        41%
        6.1
        A006850198_172656_S260_L001_R1_001
        77.7%
        39%
        7.4
        A006850198_172656_S260_L002_R1_001
        77.6%
        40%
        7.4
        A006850198_172658_S261_L001_R1_001
        89.8%
        40%
        6.9
        A006850198_172658_S261_L002_R1_001
        89.6%
        40%
        6.9
        A006850198_172660_S262_L001_R1_001
        79.4%
        40%
        6.1
        A006850198_172660_S262_L002_R1_001
        79.3%
        40%
        6.1
        A006850198_172662_S263_L001_R1_001
        76.2%
        40%
        5.9
        A006850198_172662_S263_L002_R1_001
        76.0%
        40%
        5.9
        A006850198_172664_S264_L001_R1_001
        82.6%
        41%
        7.7
        A006850198_172664_S264_L002_R1_001
        82.3%
        41%
        7.7
        A006850198_172666_S265_L001_R1_001
        79.3%
        36%
        5.9
        A006850198_172666_S265_L002_R1_001
        79.1%
        36%
        5.9
        A006850198_172668_S266_L001_R1_001
        77.1%
        41%
        6.3
        A006850198_172668_S266_L002_R1_001
        76.9%
        41%
        6.3
        A006850198_172670_S267_L001_R1_001
        75.4%
        40%
        5.4
        A006850198_172670_S267_L002_R1_001
        75.3%
        40%
        5.4
        A006850198_172672_S268_L001_R1_001
        76.0%
        41%
        5.3
        A006850198_172672_S268_L002_R1_001
        75.8%
        41%
        5.3
        A006850198_172674_S269_L001_R1_001
        78.7%
        40%
        6.1
        A006850198_172674_S269_L002_R1_001
        78.5%
        40%
        6.1
        A006850198_172676_S270_L001_R1_001
        80.2%
        41%
        5.6
        A006850198_172676_S270_L002_R1_001
        79.9%
        41%
        5.6
        A006850198_172678_S271_L001_R1_001
        83.6%
        42%
        7.4
        A006850198_172678_S271_L002_R1_001
        83.4%
        42%
        7.4
        A006850198_172680_S272_L001_R1_001
        81.9%
        41%
        6.2
        A006850198_172680_S272_L002_R1_001
        81.6%
        41%
        6.2
        A006850198_172682_S273_L001_R1_001
        77.5%
        40%
        6.8
        A006850198_172682_S273_L002_R1_001
        77.3%
        40%
        6.8
        A006850198_172684_S274_L001_R1_001
        79.5%
        41%
        5.6
        A006850198_172684_S274_L002_R1_001
        79.2%
        41%
        5.6
        A006850198_172686_S275_L001_R1_001
        87.9%
        34%
        6.6
        A006850198_172686_S275_L002_R1_001
        87.7%
        34%
        6.6
        A006850198_172688_S276_L001_R1_001
        91.7%
        40%
        6.2
        A006850198_172688_S276_L002_R1_001
        91.6%
        40%
        6.2
        A006850198_172690_S277_L001_R1_001
        73.2%
        40%
        5.5
        A006850198_172690_S277_L002_R1_001
        73.1%
        40%
        5.5
        A006850198_172692_S278_L001_R1_001
        77.3%
        40%
        6.2
        A006850198_172692_S278_L002_R1_001
        77.1%
        40%
        6.2
        A006850198_172694_S279_L001_R1_001
        86.6%
        36%
        4.5
        A006850198_172694_S279_L002_R1_001
        86.5%
        36%
        4.5
        A006850198_172696_S280_L001_R1_001
        85.4%
        40%
        6.3
        A006850198_172696_S280_L002_R1_001
        85.2%
        40%
        6.3
        A006850198_172698_S281_L001_R1_001
        91.4%
        31%
        6.1
        A006850198_172698_S281_L002_R1_001
        91.4%
        31%
        6.1
        A006850198_172700_S282_L001_R1_001
        79.1%
        40%
        5.7
        A006850198_172700_S282_L002_R1_001
        78.9%
        40%
        5.7
        A006850198_172703_S283_L001_R1_001
        77.8%
        33%
        5.0
        A006850198_172703_S283_L002_R1_001
        77.7%
        33%
        5.0
        A006850198_172705_S284_L001_R1_001
        91.2%
        32%
        6.4
        A006850198_172705_S284_L002_R1_001
        91.1%
        32%
        6.4
        A006850198_172707_S285_L001_R1_001
        70.7%
        36%
        6.4
        A006850198_172707_S285_L002_R1_001
        70.6%
        37%
        6.4
        A006850198_172709_S286_L001_R1_001
        83.3%
        39%
        5.2
        A006850198_172709_S286_L002_R1_001
        83.1%
        39%
        5.2
        A006850198_172711_S287_L001_R1_001
        83.7%
        40%
        5.2
        A006850198_172711_S287_L002_R1_001
        83.5%
        40%
        5.2
        A006850198_172713_S288_L001_R1_001
        79.6%
        38%
        5.8
        A006850198_172713_S288_L002_R1_001
        79.4%
        38%
        5.8
        A006850198_172715_S289_L001_R1_001
        90.3%
        39%
        8.0
        A006850198_172715_S289_L002_R1_001
        90.2%
        39%
        8.0
        A006850198_172717_S290_L001_R1_001
        92.2%
        34%
        5.6
        A006850198_172717_S290_L002_R1_001
        92.2%
        34%
        5.6
        A006850198_172719_S291_L001_R1_001
        79.8%
        39%
        6.1
        A006850198_172719_S291_L002_R1_001
        79.8%
        39%
        6.1
        A006850198_172721_S292_L001_R1_001
        89.8%
        33%
        5.8
        A006850198_172721_S292_L002_R1_001
        89.8%
        33%
        5.8
        A006850201_172476_S21_L001_R1_001
        41.8%
        36%
        9.0
        A006850201_172504_S22_L001_R1_001
        41.7%
        36%
        6.8
        A006850201_172509_S23_L001_R1_001
        38.9%
        35%
        5.2
        A006850201_172511_S24_L001_R1_001
        42.8%
        36%
        6.6
        A006850201_172513_S25_L001_R1_001
        34.2%
        34%
        6.2
        A006850201_172515_S26_L001_R1_001
        67.9%
        41%
        5.1
        A006850201_172517_S27_L001_R1_001
        63.4%
        41%
        6.0
        A006850201_172519_S28_L001_R1_001
        53.3%
        39%
        5.2
        A006850201_172539_S29_L001_R1_001
        59.6%
        39%
        4.9
        A006850201_172541_S30_L001_R1_001
        59.1%
        39%
        4.7
        A006850201_172543_S31_L001_R1_001
        57.8%
        39%
        5.7
        A006850201_172545_S32_L001_R1_001
        60.6%
        40%
        5.6
        A006850201_172561_S33_L001_R1_001
        62.1%
        41%
        4.9
        A006850201_172563_S34_L001_R1_001
        58.8%
        40%
        6.9
        A006850201_172565_S35_L001_R1_001
        51.0%
        37%
        5.6
        A006850201_172571_S36_L001_R1_001
        59.3%
        40%
        5.9
        A006850201_172573_S37_L001_R1_001
        57.3%
        39%
        5.9
        A006850201_172575_S38_L001_R1_001
        49.0%
        31%
        4.2
        A006850201_172642_S39_L001_R1_001
        76.4%
        40%
        7.8

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        loading..

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        loading..

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        loading..

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        loading..

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        loading..

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        loading..

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.